TIPP_plastid conda recipe (#51644)

* Committer: Anupam Gautam <[email protected]> TIPP_plastid is a User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/meta.yaml Co-authored-by: Martin Grigorov <[email protected]> * Committer: Anupam Gautam <[email protected]> suggestion incorporated * Committer: Anupam Gautam <[email protected]> updated meta and build. * GenEra conda recipes * removed genera files * adjusted python * update * update * Update meta.yaml * update * update * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Anupam Gautam <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: richard-burhans <[email protected]> Co-authored-by: Anupam Gautam <[email protected]>
bioconda · Nov 25, 2024 · 557ed37 · 557ed37
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diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh
@@ -0,0 +1,69 @@
+#!/bin/bash
+
+# Exit on any error
+set -ex
+
+# Define variables for directories
+# define kmc directory  
+
+KMC_DIR="src/kmc3"
+
+mkdir $KMC_DIR/bin
+cp $BUILD_PREFIX/bin/kmc* $KMC_DIR/bin/
+cp $BUILD_PREFIX/lib/libkmc_core.a $KMC_DIR/bin/
+
+# Build seqtk
+SEQTK_DIR="src/seqtk"
+cd "$SEQTK_DIR"
+
+export C_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
+
+make CC=${CC} CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" all -j "${CPU_COUNT}"
+
+# Go back to the src directory
+cd ..
+
+# Compile readskmercount as an object first if it doesn't have a main
+${CXX}  -c readskmercount.opt.cpp -I./kmc3
+
+# Then link it to create the executable
+${CXX}  -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread
+
+# Copy everything to the Conda environments bin directory to ensure they're accessible
+echo "Copying binaries to PREFIX..."
+mkdir -p $PREFIX/bin
+mkdir -p $PREFIX/bin/kmc3
+mkdir -p $PREFIX/bin/seqtk
+
+for file in *.pl; do
+  sed -i.bak '1 s|^#!/usr/bin/perl$|#!/usr/bin/env perl|' "$file"
+done
+
+cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r TIPP_plastid.v2.1.pl TIPP_telomere.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
+cp -r kmc3/bin $PREFIX/bin/kmc3/
+cp seqtk/seqtk $PREFIX/bin/seqtk/
+
+echo "Installation completed successfully."
+echo "Copying activation and deactivation scripts..."
+mkdir -p $PREFIX/etc/conda/activate.d
+mkdir -p $PREFIX/etc/conda/deactivate.d
+
+# Add TIPP and related tools to the PATH
+
+cat << EOF > $PREFIX/etc/conda/activate.d/tipp.sh
+# Set the current path to the conda environment's bin directory
+export CURRENT_PATH=\$CONDA_PREFIX/bin
+
+# Add TIPP and related tools to the PATH
+export PATH=\$CURRENT_PATH:\$PATH
+export PATH=\$CURRENT_PATH/seqtk:\$PATH
+export PATH=\$CURRENT_PATH/kmc3/bin:\$PATH
+EOF
+
+cat << EOF > $PREFIX/etc/conda/deactivate.d/tipp.sh
+# Remove the current conda environment's bin directory from PATH
+export PATH=\$(echo \$PATH | sed -e "s|$CONDA_PREFIX/bin:||g")
+EOF
+
+echo "Installation completed successfully."
diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml
@@ -0,0 +1,55 @@
+package:
+  name: tipp
+  version: "1.1.0"
+
+source:
+  git_url: https://github.com/Wenfei-Xian/TIPP.git
+  git_tag: v1.1.0
+  sha256: a3e57e709c206b742a954524b3f1d304d435e6f3cbe85617ade745b8ef5d5d7f
+
+build:
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('tipp', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}  # For compiling C++ code
+    - make
+    - kmc
+  host:
+    - python >=3.8,<3.9
+    - zlib
+    - perl
+  run:
+    - python >=3.8,<3.9
+    - libxcrypt
+    - tiara
+    - graphaligner =1.0.17
+    - flye
+    - minimap2 =2.26
+    - spoa =4.1.4
+    - mcl =22.282
+    - r-pheatmap =1.0.12
+    - r-igraph =1.5.1
+    - bioconductor-biostrings =2.68.1
+    - r-stringdist =0.9.10
+    - r-ggplot2 =3.4.4
+    - trf =4.09.1
+    - zlib
+    - perl
+test:
+  commands:
+    - TIPP_plastid.v2.1.pl -h
+    - TIPP_telomere.pl -h
+
+about:
+  home: https://github.com/Wenfei-Xian/TIPP
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
+  summary: "TIPP: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data"
+
+extra:
+  skip-lints:
+    - uses_vcs_url